When was the current pagination of the Gemara finalized? It seems that it was before the Vilna print, though it seems from different Acharonim (the Rama, etc.) quoting the Mordechai that the Mordechai used to be referred by page number.

Also, was any other Rishon ever printed on the side of the Gemara instead of Tosfos?

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The standard pagination and layout of the Gemara follows that of Daniel Bomberg's edition of 1520-22, which was the first time that Shas was printed as a complete set. (Earlier Jewish printers, including the famous Soncino family, had produced only individual volumes.) A notable difference is that Berachos has 66 pages as compared to today's 64; that change was made in his next edition, approximately 1526-39.